High transcriptome plasticity drives phosphate starvation responses in tomato.

Tomato is an important vegetable crop and fluctuating available soil phosphate (Pi) level elicits several morpho-physiological responses driven by underlying molecular responses. Therefore, understanding these molecular responses at the gene and isoform levels has become critical in the quest for developing crops with improved Pi use efficiency. A quantitative time-series RNA-seq analysis was performed to decipher the global transcriptomic changes that accompany Pi starvation in tomato. Apart from changes in the expression levels of genes, there were also alterations in the expression of alternatively-spliced transcripts. Physiological responses such as anthocyanin accumulation, reactive oxygen species generation and cell death are obvious 7 days after Pi deprivation accompanied with the maximum amount of transcriptional change in the genome making it an important stage for in-depth study while studying Pi stress responses (PSR). Our study demonstrates that transcriptomic changes under Pi deficiency are dynamic and complex in tomato. Overall, our study dwells on the dynamism of the transcriptome in eliciting a response to adapt to low Pi stress and lays it bare. Findings from this study will prove to be an invaluable resource for researchers using tomato as a model for understanding nutrient deficiency.

Genome-wide identification and characterization of SPX-domain-containing protein gene family in Solanum lycopersicum.

The SYG1, PHO81, and XPR1 (SPX) domain is named after the suppressor of yeast gpa1 (Syg1), yeast phosphatase (Pho81) and the human Xenotropic and Polytrophic Retrovirus receptor1 (XPR1). SPX-domain-containing proteins play pivotal roles in maintaining phosphate ions (Pi) homeostasis in plant. This study was to genome-wide identification and analysis of Solanum lycopersicum SPX-domain-containing protein gene family. The Solanum lycopersicum genome contains 19 SPX-domain-containing protein genes. These SPX-domain-containing protein genes were located in seven of the 12 chromosomes. According to the different conserved domains, the proteins encoded by those genes could be divided into four SPX-domain-containing protein families, which included SPX Family, SPX-ERD1/XPR1/SYG1(SPX-EXS) Family, SPX-Major Facilitator Superfamily (SPX-MFS) Family and SPX-Really Interesting New Gene (SPX-RING) Family. Phylogenetic analysis of SPX-domain-containing protein genes in Arabidopsis thaliana, Solanum tuberosum, Capsicum annuum and Solanum lycopersicum classified these genes into eight clades. Expression profiles derived from transcriptome (RNA-seq) data analysis showed 19 SPX-domain-containing protein genes displayed various expression patterns. SPX-domain-containing protein may play different roles in phosphate nutrition of Solanum lycopersicum different tissues and development stages. And, this study can provide the selection of candidate genes for functional research and genome editing in Solanum lycopersicum phosphate ions (Pi) nutrition.

A CRISPR/Cas9 deletion into the phosphate transporter SlPHO1;1 reveals its role in phosphate nutrition of tomato seedlings.

In vascular (Arabidopsis thaliana) and non-vascular (Physcomitrella patens) plants, PHOSPHATE 1 (PHO1) homologs play important roles in the acquisition and transfer of phosphate. The tomato genome contains six genes (SlPHO1;1-SlPHO1;6) homologous to AtPHO1. The six proteins have typical characteristics of the plant PHO1 family, such as the three Syg1/Pho81/XPRI (SPX) subdomains in the N-terminal portion and one ERD1/XPR1/SYG1 (EXS) domain in the C-terminal portion. Phylogenetic analysis revealed that the SlPHO1 family is subdivided into three clusters. A pairwise comparison indicated that SlPHO1;1 showed the highest level of sequence identity/similarity (67.39/76.21%) to AtPHO1. SlPHO1;1 deletion mutants induced by clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 displayed typical phenotypes of Pi starvation, such as decreased shoot fresh weight and increased root fresh weight, therefore having a greater root-to-shoot ratio. Mutants also accumulated more anthocyanin and had more soluble Pi content in the root and less in the shoot. These results indicate that SlPHO1;1 plays an important role in Pi transport in the tomato at seedling stage.

Three Fatty Acyl-Coenzyme A Reductases, BdFAR1, BdFAR2 and BdFAR3, are Involved in Cuticular Wax Primary Alcohol Biosynthesis in Brachypodium distachyon.

Plant cuticular wax is a heterogeneous mixture of very long chain fatty acids (VLCFAs) and their derivatives. Primary alcohols are the dominant wax components throughout leaf development of Brachypodium distachyon (Brachypodium). However, the genes involved in primary alcohol biosynthesis have not been investigated and their exact biological function remains unclear in Brachypodium to date. Here, we monitored the leaf wax profile and crystal morphology during Brachypodium leaf morphogenesis, and isolated three Brachypodium fatty acyl-CoA reductase (FAR) genes, named BdFAR1, BdFAR2 and BdFAR3, then analyzed their biochemical activities, substrate specificities, expression patterns, subcellular localization and stress induction. Transgenic expression of BdFAR genes in yeast (Saccharomyces cerevisiae), tomato (Solanum lycopersicum), Arabidopsis (Arabidopsis thaliana) and Brachypodium increased the production of primary alcohols. The three BdFAR genes were preferentially expressed in Brachypodium aerial tissues, consistent with known sites of wax primary alcohol deposition, and localized in the endoplasmic reticulum (ER) in Arabidopsis protoplasts. Finally, expression of the BdFAR genes was induced by drought, cold and ABA treatments, and drought stress significantly increased cuticular wax accumulation in Brachypodium. Taken together, these results indicate that the three BdFAR genes encode active FARs involved in the biosynthesis of Brachypodium wax primary alcohols and respond to abiotic stresses.